7A01

The Halastavi arva virus intergenic region IRES promotes translation by the simplest possible initiation mechanism


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The Halastavi arva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism.

Abaeva, I.S.Vicens, Q.Bochler, A.Soufari, H.Simonetti, A.Pestova, T.V.Hashem, Y.Hellen, C.U.T.

(2020) Cell Rep 33: 108476-108476

  • DOI: https://doi.org/10.1016/j.celrep.2020.108476
  • Primary Citation of Related Structures:  
    6ZVK, 7A01

  • PubMed Abstract: 

    Dicistrovirus intergenic region internal ribosomal entry sites (IGR IRESs) do not require initiator tRNA, an AUG codon, or initiation factors and jumpstart translation from the middle of the elongation cycle via formation of IRES/80S complexes resembling the pre-translocation state. eEF2 then translocates the [codon-anticodon]-mimicking pseudoknot I (PKI) from ribosomal A sites to P sites, bringing the first sense codon into the decoding center. Halastavi árva virus (HalV) contains an IGR that is related to previously described IGR IRESs but lacks domain 2, which enables these IRESs to bind to individual 40S ribosomal subunits. By using in vitro reconstitution and cryoelectron microscopy (cryo-EM), we now report that the HalV IGR IRES functions by the simplest initiation mechanism that involves binding to 80S ribosomes such that PKI is placed in the P site, so that the A site contains the first codon that is directly accessible for decoding without prior eEF2-mediated translocation of PKI.


  • Organizational Affiliation

    INSERM U1212 Acides Nucléiques: Régulations Naturelle et Artificielle, Institut Européen de Chimie et Biologie, Université de Bordeaux, Pessac 33607, France. Electronic address: yaser.hashem@inserm.fr.


Macromolecules

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinE [auth p2]69Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U001 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
eL14F [auth k2]131Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24G [auth l2]63Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinH [auth m2]119Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26I [auth o2]134Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
uL15J [auth q2]147Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29K [auth r2]75Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TN82 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
uL4L [auth t2]362Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eL31M [auth u2]107Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
eL32N [auth v2]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN UL13O [auth w2]199Oryctolagus cuniculusMutation(s): 2 
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Find proteins for G5B8P1 (Heterocephalus glaber)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL33P [auth x2]109Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL34Q [auth y2]114Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U945 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinR [auth 92]244Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL29S [auth A2]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36T [auth B2]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37U [auth C2]86Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eL39V [auth D2]50Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SYU7 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL40W [auth E2]52Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
eL42X [auth F2]104Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5Y [auth G2]292Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
uL22Z [auth H2]153Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TVT6 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eL43AA [auth I2]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinBA [auth J2]125Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0CA [auth K2]198Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10 (Predicted)DA [auth L2]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinEA [auth M2]163Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L6e_N domain-containing proteinFA [auth R2]35Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL18GA [auth S2]187Oryctolagus cuniculusMutation(s): 0 
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GTEx:  ENSG00000063177 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6HA [auth T2]201Oryctolagus cuniculusMutation(s): 2 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
uL30IA [auth U2]225Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL8JA [auth V2]241Oryctolagus cuniculusMutation(s): 0 
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GTEx:  ENSG00000148303 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinKA [auth W2]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10 (Predicted)LA [auth X2]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11MA [auth Y2]169Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14NA [auth 02]138Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15OA [auth 12]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27PA [auth 22]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL19QA [auth 32]180Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinRA [auth 42]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
uL3SA [auth 52]394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S RIBOSOMAL PROTEIN EL20TA [auth 62]175Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
eL21UA [auth 72]159Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L22VA [auth 82]99Oryctolagus cuniculusMutation(s): 6 
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES30XA [auth s3]43Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P62866 (Bos taurus)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L30YA [auth 13]94Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27aZA [auth Q3]188Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SK22 (Oryctolagus cuniculus)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S11AB [auth G3]153Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TRM4 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS13BB [auth G5]137Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein RACK1CB [auth a3]313Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SJB4 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinDB [auth a5]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T1F0 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS19EB [auth A3]127Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U0Q2 (Oryctolagus cuniculus)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S23FB [auth T3]141Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ47 (Oryctolagus cuniculus)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S_SA_C domain-containing proteinGB [auth U3]208Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJH8 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aHB [auth V3]213Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
S5 DRBM domain-containing proteinIB [auth W3]218Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60s ribosomal protein l41JB [auth X3]23Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S3KB [auth Y3]227Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
UniProt
Find proteins for G1TNM3 (Oryctolagus cuniculus)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4,40S ribosomal protein S4LB [auth j3]262Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aMB [auth J5]129Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TG89 (Oryctolagus cuniculus)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5NB [auth N3]191Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KMN4 (Oryctolagus cuniculus)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6OB [auth b3]237Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TM55 (Oryctolagus cuniculus)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinPB [auth B3]141Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGX4 (Oryctolagus cuniculus)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS28QB [auth f3]64Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS15RB [auth F3]150Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SP51 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8SB [auth c3]206Oryctolagus cuniculusMutation(s): 1 
UniProt
Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinTB [auth C3]129Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9 (Predicted)UB [auth d3]185Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES21VB [auth D3]83Oryctolagus cuniculusMutation(s): 5 
UniProt
Find proteins for A0A1Z5KTU7 (Ornithodoros moubata)
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12WB [auth e3]124Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SFR8 (Oryctolagus cuniculus)
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
S10_plectin domain-containing proteinXB [auth E3]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T168 (Oryctolagus cuniculus)
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein uS14YB [auth H3]53Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7M4 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinZB [auth H5]141Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TN62 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES7AC [auth P3]189Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A6H769 (Bos taurus)
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_S10 domain-containing proteinBC [auth I3]104Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9CX53 (Oryctolagus cuniculus)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24CC [auth I5]126Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9CBF4 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27DC [auth L3]83Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein eS25EC [auth M3]75Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDB3 (Oryctolagus cuniculus)
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN ES26FC [auth O3]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for Q56JV1 (Bos taurus)
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13GC [auth a7]210Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPV0 (Oryctolagus cuniculus)
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Entity ID: 1
MoleculeChains LengthOrganismImage
INTERNAL RIBOSOME ENTRY SITEA [auth E1]153Halastavi arva RNA virus
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Entity ID: 2
MoleculeChains LengthOrganismImage
28S RIBOSOMAL RNAB [auth e2]3,825Oryctolagus cuniculus
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Entity ID: 3
MoleculeChains LengthOrganismImage
5.8S RIBOSOMAL RNAC [auth h2]156Oryctolagus cuniculus
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